The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase
Abstract
The recently described molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method for calculating free energies is applied to a congeneric series of 16 ligands to p38 MAP kinase whose binding constants span approximately 2 orders of magnitude. These compounds have previously been used to test and compare other free energy calculation methods, including thermodynamic integration (TI), OWFEG, ChemScore, PLPScore, and Dock Energy Score. We find that the MM-PBSA performs relatively poorly for this set of ligands, yielding results much inferior to those from TI or OWFEG, inferior to Dock Energy Score, and not appreciably better than ChemScore or PLPScore but at an appreciably larger computational cost than any of these other methods. This suggests that one should be selective in applying the MM-PBSA method and that for systems that are amenable to other free energy approaches, these other approaches may be preferred. We also examine the single simulation approximation for MM-PBSA, whereby the required ligand and protein trajectories are extracted from a single MD simulation rather than two separate MD runs. This assumption, sometimes used to speed the MM-PBSA calculation, is found to yield significantly inferior results with only a moderate net percentage reduction in total simulation time.
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Cites
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Charifson, P. S., Corkery, J. J., Murcko, M. A., & Walters, W. P. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm990352k · Cited by 698
Cited by
Hou, T., Wang, J., Li, Y., & Wang, W. (2011) · Journal of Chemical Information and Modeling · doi:10.1021/ci100275a · Cited by 2,773
Fast and accurate predictions of binding free energies using MM‐PBSA and MM‐GBSA
Rastelli, G., Rio, A. D., Degliesposti, G., & Sgobba, M. (2010) · Journal of Computational Chemistry · doi:10.1002/jcc.21372 · Cited by 828
Combining docking and molecular dynamic simulations in drug design
Alonso, H., Bliznyuk, A. A., & Gready, J. E. (2006) · Medicinal Research Reviews · doi:10.1002/med.20067 · Cited by 759
Lyne, P. D., Lamb, M. L., & Saeh, J. C. (2006) · Journal of Medicinal Chemistry · doi:10.1021/jm060522a · Cited by 699
Efficient Drug Lead Discovery and Optimization
Jorgensen, W. L. (2009) · Accounts of Chemical Research · doi:10.1021/ar800236t · Cited by 649
Advances and Challenges in Protein-Ligand Docking
Huang, S.-Y., & Zou, X. (2010) · International Journal of Molecular Sciences · doi:10.3390/ijms11083016 · Cited by 639
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
Mobley, D. L., & Dill, K. A. (2009) · Structure · doi:10.1016/j.str.2009.02.010 · Cited by 584
Huang, S.-Y., Grinter, S. Z., & Zou, X. (2010) · Physical Chemistry Chemical Physics · doi:10.1039/c0cp00151a · Cited by 508
Nguyen, C. N., Kurtzman Young, T., & Gilson, M. K. (2012) · The Journal of Chemical Physics · doi:10.1063/1.4733951 · Cited by 324
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
Mobley, D. L., Graves, A. P., Chodera, J. D., McReynolds, A. C., Shoichet, B. K., & Dill, K. A. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.06.002 · Cited by 310
Hazardous Shortcuts in Standard Binding Free Energy Calculations
Blazhynska, M., Goulard Coderc de Lacam, E., Chen, H., Roux, B., & Chipot, C. (2022) · The Journal of Physical Chemistry Letters · doi:10.1021/acs.jpclett.2c01490 · Cited by 27
Metadata
- Authors
- Pearlman, D. A.
- Venue
- Journal of Medicinal Chemistry
- Publisher
- American Chemical Society (ACS)
- Published
- 2005-11-05
- Volume
- 48
- Issue
- 24
- Pages
- 7796-7807
- ISSN
- 0022-2623 (ISSN-L)
- 1520-4804
- OpenAlex
- W1995807192
- Cited by
- 193
- References
- 2
- FWCI
- 10.67
- Type
- journal article
- Language
- en
- Open access
- closed
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